## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("ssviz") ## ----loadingPackage,message=FALSE--------------------------------------------- library(ssviz) ## ----loaddata----------------------------------------------------------------- data(ssviz) ## ----loading-bam,tidy=TRUE,warning=FALSE-------------------------------------- bam.files<-dir(system.file("extdata", package="ssviz"), full=TRUE, patt="bam$") ctrlbam<-readBam(bam.files[1]) treatbam<-readBam(bam.files[2]) ## ----viewobject--------------------------------------------------------------- ctrlbam ## ----gettingReadCounts,warning=FALSE------------------------------------------ ctrl.count<-getCountMatrix(ctrlbam) treat.count<-getCountMatrix(treatbam) ## ----gettingReadCounts2,warning=FALSE----------------------------------------- ctrl.count[1,] ## ----plotdistro1,tidy=TRUE,eval=FALSE----------------------------------------- # plotDistro(list(ctrl.count), type="qwidth", samplenames=c("Control"), ncounts=counts[1]) ## ----plotdistro2,tidy=TRUE,eval=FALSE,warning=FALSE--------------------------- # plotDistro(list(ctrl.count, treat.count), type="qwidth", samplenames=c("Control","Treatment"), ncounts=counts) ## ----regiondens,eval=FALSE---------------------------------------------------- # region<-'chr1:3015526-3080526' # plotRegion(list(ctrl.count), region=region) ## ----pingpong,eval=FALSE------------------------------------------------------ # pp.ctrl<-pingpong(pctrlbam.count) # plotPP(list(pp.ctrl), samplenames=c("Control")) ## ----ntfreq,eval=FALSE-------------------------------------------------------- # pctrlbam.count<-getCountMatrix(pctrlbam) # freq.ctrl<-ntfreq(pctrlbam.count, ntlength=10) # plotFreq(freq.ctrl) ## ----------------------------------------------------------------------------- sessionInfo()